Fix edam syntax input+output is singular (e7a60294) · Commits · Debian Med / fastaq

debian/upstream/edam

+67 −67

Original line number	Diff line number	Diff line
		@@ -6,75 +6,75 @@ scopes:
		- name: add_indels
		function:
		- Sequence mutation and randomisation
		inputs:
		input:
		- data: Sequence
		formats: [FASTA, FASTQ]
		outputs:
		output:
		- data: Sequence
		formats: [FASTA, FASTQ]
		- name: caf_to_fastq
		function:
		- Formatting
		inputs:
		input:
		- data: Sequence assembly report
		formats: [CAF]
		outputs:
		output:
		- data: Sequence
		formats: [FASTQ]
		- name: capillary_to_pairs
		function:
		- Sequence file editing
		inputs:
		input:
		- data: Sequence
		formats: [FASTA]
		outputs:
		output:
		- data: Sequence
		formats: [FASTA]
		- name: chunker
		function:
		- Splitting
		inputs:
		input:
		- data: Sequence
		formats: [FASTA, FASTQ]
		outputs:
		output:
		- data: Sequence
		formats: [FASTA, FASTQ]
		- name: count_sequences
		function:
		- Data handling
		inputs:
		input:
		- data: Sequence
		formats: [FASTA, FASTQ]
		outputs:
		output:
		- data: Sequence
		formats: [FASTA, FASTQ]
		- name: deinterleave
		function:
		- Splitting
		inputs:
		input:
		- data: Sequence
		formats: [FASTA]
		outputs:
		output:
		- data: Sequence
		formats: [FASTA]
		- name: enumerate_names
		function:
		- Sequence file editing
		inputs:
		input:
		- data: Sequence
		formats: [FASTA, FASTQ]
		outputs:
		output:
		- data: Sequence
		formats: [FASTA, FASTQ]
		- name: expand_nucleotides
		function:
		- Sequence generation (nucleic acid)
		inputs:
		input:
		- data: Sequence
		formats:
		- FASTA
		- FASTQ
		outputs:
		output:
		- data: Sequence
		formats:
		- FASTA
		@@ -82,21 +82,21 @@ scopes:
		- name: fasta_to_fastq
		function:
		- Formatting
		inputs:
		input:
		- data: Sequence
		formats:
		- FASTA
		- qual
		outputs:
		output:
		- data: Sequence
		formats: [FASTQ]
		- name: filter
		function:
		- Sequence file editing
		inputs:
		input:
		- data: Sequence
		formats: [FASTA, FASTQ]
		outputs:
		output:
		- data: Sequence
		formats:
		- FASTA
		@@ -104,45 +104,45 @@ scopes:
		- name: get_ids
		function:
		- ID retrieval
		inputs:
		input:
		- data: Sequence
		formats: [FASTA, FASTQ]
		outputs:
		output:
		- data: Sequence
		formats: [FASTA, FASTQ]
		- name: get_seq_flanking_gaps
		function:
		- Sequence database search
		inputs:
		input:
		- data: Sequence
		formats: [FASTA]
		outputs:
		output:
		- data: Sequence
		formats: [FASTA]
		- name: interleave
		function:
		- Aggregation
		inputs:
		input:
		- data: Sequence
		formats: [FASTA, FASTQ]
		outputs:
		output:
		- data: Sequence
		formats: [FASTA, FASTQ]
		- name: make_random_contigs
		function:
		- Random sequence generation
		outputs:
		output:
		- data: Sequence
		formats: [FASTQ]
		- name: merge
		function:
		- Aggregation
		inputs:
		input:
		- data: Sequence
		formats:
		- FASTA
		- FASTQ
		outputs:
		output:
		- data: Sequence
		formats:
		- FASTA
		@@ -150,12 +150,12 @@ scopes:
		- name: replace_bases
		function:
		- Sequence mutation and randomization
		inputs:
		input:
		- data: Sequence
		formats:
		- FASTA
		- FASTQ
		outputs:
		output:
		- data: Sequence
		formats:
		- FASTA
		@@ -163,37 +163,37 @@ scopes:
		- name: reverse_complement
		function:
		- Nucleic acid sequence reverse and complement
		inputs:
		input:
		- data: Sequence
		formats: [FASTA, FASTQ]
		outputs:
		output:
		- data: Sequence
		formats: [FASTA, FASTQ]
		- name: scaffolds_to_contigs
		function:
		- Sequence generation (nucleic acid)
		inputs:
		input:
		- data: Sequence
		formats: [FASTA, FASTQ]
		outputs:
		output:
		- data: Sequence
		formats: [FASTA, FASTQ]
		- name: search_for_seq
		function:
		- Sequence database search
		inputs:
		input:
		- data: Sequence
		formats: [FASTA, FASTQ]
		outputs:
		output:
		- data: Sequence
		formats: [FASTA, FASTQ]
		- name: sequence_trim
		function:
		- Sequence trimming
		inputs:
		input:
		- data: Sequence
		formats: [FASTA, FASTQ]
		outputs:
		output:
		- data: Sequence
		formats:
		- FASTA
		@@ -201,12 +201,12 @@ scopes:
		- name: sort_by_size
		function:
		- Sequence file editing
		inputs:
		input:
		- data: Sequence
		formats:
		- FASTA
		- FASTQ
		outputs:
		output:
		- data: Sequence
		formats:
		- FASTA
		@@ -214,12 +214,12 @@ scopes:
		- name: split_by_base_count
		function:
		- Splitting
		inputs:
		input:
		- data: Sequence
		formats:
		- FASTA
		- FASTQ
		outputs:
		output:
		- data: Sequence
		formats:
		- FASTA
		@@ -227,12 +227,12 @@ scopes:
		- name: strip_illumina_suffix
		function:
		- Sequence file editing
		inputs:
		input:
		- data: Sequence
		formats:
		- FASTA
		- FASTQ
		outputs:
		output:
		- data: Sequence
		formats:
		- FASTA
		@@ -240,16 +240,16 @@ scopes:
		- name: to_fake_qual
		function:
		- Generation
		inputs:
		input:
		- data: Sequence
		formats: [FASTA, FASTQ]
		outputs:
		output:
		- data: Sequence
		formats: [qual]
		- name: to_fasta
		function:
		- Formatting
		inputs:
		input:
		- data: Sequence
		formats:
		- FASTA
		@@ -258,96 +258,96 @@ scopes:
		- EMBL format
		- GenBank format
		- PHYLIP format
		outputs:
		output:
		- data: Sequence
		formats: [FASTA]
		- name: to_mira_xml
		function:
		- Generation
		inputs:
		input:
		- data: Sequence
		formats:
		- FASTA
		- FASTQ
		outputs:
		output:
		- data: Sequence
		formats:
		- XML
		- name: to_orfs_gff
		function:
		- Coding region prediction
		inputs:
		input:
		- data: Sequence
		formats:
		- FASTA
		- FASTQ
		outputs:
		output:
		- data: Sequence features
		formats:
		- GFF3
		- name: to_perfect_reads
		function:
		- Generation
		inputs:
		input:
		- data: Sequence
		formats:
		- FASTA
		- FASTQ
		outputs:
		output:
		- data: Sequence
		formats:
		- FASTQ
		- name: to_random_subset
		function:
		- Random sequence generation
		inputs:
		input:
		- data: Sequence
		formats: [FASTA, FASTQ]
		outputs:
		output:
		- data: Sequence
		formats: [FASTQ]
		- name: to_tiling_bam
		function:
		- Generation
		inputs:
		input:
		- data: Sequence
		formats: [FASTA]
		outputs:
		output:
		- data: Alignment
		formats: [BAM]
		- name: translate
		function:
		- DNA translation
		inputs:
		input:
		- data: Sequence
		formats: [FASTA, FASTQ]
		outputs:
		output:
		- data: Sequence
		formats: [FASTA]
		- name: trim_Ns_at_end
		function:
		- Sequence trimming
		inputs:
		input:
		- data: Sequence
		formats: [FASTA, FASTQ]
		outputs:
		output:
		- data: Sequence
		formats: [FASTA, FASTQ]
		- name: trim_contigs
		function:
		- Sequence trimming
		inputs:
		input:
		- data: Sequence
		formats: [FASTA, FASTQ]
		outputs:
		output:
		- data: Sequence
		formats: [FASTA, FASTQ]
		- name: trim_ends
		function:
		- Sequence trimming
		inputs:
		input:
		- data: Sequence
		formats: [FASTA, FASTQ]
		outputs:
		output:
		- data: Sequence
		formats: [FASTA, FASTQ]